rs2181033

Variant names:

• chr9-114935551-A-G
• rs2181033
• ENST00000648852.1:n.198+13953A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648852.1(DELEC1):​n.198+13953A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,080 control chromosomes in the GnomAD database, including 9,287 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (9287 hom., cov: 32)
• Consequence: DELEC1 ENST00000648852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628
• Publications: 8 publications found

Genes affected

DELEC1 (HGNC:23658): (deleted in esophageal cancer 1) The function of this gene is not known. This gene is located in a region commonly deleted in esophageal squamous cell carcinomas. Gene expression is reduced or absent in these carcinomas and thus this is a candidate tumor suppressor gene for esophageal squamous cell carcinomas. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648852.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DELEC1	ENST00000648852.1		n.198+13953A>G		intron	N/A
	DELEC1	ENST00000649565.1		n.226-34033A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51831 AN: 151962 Hom.: 9277 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.343

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.341 AC: 51864 AN: 152080 Hom.: 9287 Cov.: 32 AF XY: 0.344 AC XY: 25582 AN XY: 74334

African (AFR) AF: 0.233 AC: 9674 AN: 41522

American (AMR) AF: 0.441 AC: 6727 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1367 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1318 AN: 5158

South Asian (SAS) AF: 0.386 AC: 1861 AN: 4820

European-Finnish (FIN) AF: 0.375 AC: 3966 AN: 10564

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25708 AN: 67966

Other (OTH) AF: 0.348 AC: 732 AN: 2106

Alfa AF: 0.371 Hom.: 5526

Bravo AF: 0.339

Asia WGS AF: 0.379 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.71
PhyloP100		-0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2181033; hg19: chr9-117697831;